Microorganisms contain a large number of biocatalysts, which are of great potential in industrial applications. However, the traditional cultural approaches can obtain only less than 1% of microorganisms. As a culture-independent method, metagenomics is an advanced solution by means of extracting all microbial genomic DNAs in certain environmental habitat, constructing and screening metagenomic libraries to seek novel functional genes. It serves as an effective tool for studying these uncultured microorganisms. Therefore, mining novel biocatalysts from metagenome has drawn the attention of researchers in the world. In this paper, environment sample category, genomic DNA extraction, library construction and screening strategies were reviewed. Recent examples of isolated biocatalysts from metagenomic libraries were presented. Future research directions of metagenomics were also discussed.
Biocatalysis ; DNA ; Genomic Library ; Metagenomics ; trends

OBJECTIVETo investigate the genetic diversity and structure of Dendrobium huoshanense, a (CT)n enriched microsatellite library was constructed using a magnetic beads enrichment procedure.

METHODThe 3'-biotinylated oligonucleotide probe was used to hybridize with the digested D. huoshanense genomic DNA fragments whose both ends were ligated with adaptors. The hybridized complex was then combined with the streptavidin-coated magnetic beads. The captured microsatellite fragments were eluted, collected and cloned into pMD19-T vector. The recombinant plasmids were transformed into Escherichia coli DH5alpha competent cells. The clones that yielded two or more bands contained microsatellite fractions. Positive clones were screened and sequenced. Thirty pairs of primers were designed and synthesized. Polymorphism at each locus was determined using 24 individuals from a natural population from Huoshan county town in Anhui province.

RESULTTwelve polymorphic microsatellite loci from the microsatellite-enriched genomic library were newly developed across 24 D. huoshanense individuals. In total, 65 alleles were identified, and the number of alleles per locus ranged from 2 to 8. The mean observed and expected heterozygosities were 0.500 and 0.638, respectively. Two loci significantly deviated from Hardy-Weinberg equilibrium (P<0.05), which could be due to the presence of null alleles. Furthermore, three of twelve loci showed significant linkage disequilibrium (P<0.05).

CONCLUSIONThese results suggest that the identified polymorphic microsatellite markers will be useful in population genetic studies of D. huoshanense.

Hv-S/TPK gene, a resistance related gene to powdery mildew, was cloned by using genechip, and its expression was upregulated after the inoculation of Blumeria graminis to Haynaldia villosa. Using the specific primers of Hv-S/TPK to screen a genomic TAC (Transformation-competent artificial chromosome) library of translocation line 6VS/6AL, a positive TAC was screened. A 5-kb fragment containing Hv-S/TPK was subcloned and identified. This 5160-bp fragment (GenBank Accession No. EU153366) was determined by specific primer walking. The analysis of Hv-S/TPK genomic sequence showed three introns and four extrons between start code and stop code. In the promoter region of Hv-S/TPK, there were W-box and OCS-like elements which were the elements related to disease resistance. In this study, the positive TAC clone was used to as probe in situ hybridized to mitotic metaphase chromosomes of translocation line. The result of fluorescence in situ hybridization (FISH) indicated that the TAC clone containing Hv-S/TPK was from Haynaldia villosa chromosome.
Base Sequence ; Chromosomes, Artificial ; Cloning, Molecular ; Genomic Library ; Molecular Sequence Data ; Plant Diseases ; genetics ; Poaceae ; genetics ; Protein-Serine-Threonine Kinases ; genetics ; Serine ; genetics ; Translocation, Genetic ; Triticum ; genetics ; virology

OBJECTIVE: To construct the genomic library of Raji cells and screen it by EBV DNA probe. METHODS: High molecular weight genomic DNA of Raji cells was digested by restriction enzyme BamHI. DNA fragments ranging from 9 to 23 kb were recovered by agarose gel electrophoresis, which were ligated with Lambda DASH II vector BamHI arms pre-treated with calf intestine alkaline phosphatase (CIAP). Ligated DNA was packed in vitro using Gigapack III gold packaging extract. The library was plated on XL1-blue MRA (P2) host strain.Titering and screening of the Raji genomic library were performed. RESULTS: The primary titer of the Raji genomic library was 1.8 x 10(5) pfu/mL, while that of the amplified library was 2.8 x 10(8) pfu/mL. Plaques (1 x 10(5)) were screened with (32)P-labeled EBV DNA probe(EBV genome 5-3271), 4 positive clones were obtained, and 1 of the 4 positive clones was picked out randomly for the second round of plaque screening. All the phage plaques were positive. DNA of the positive clone was extracted and was digested with BamHI. The length of the inserted fragment was 8.5 kb. Sequencing and BLAST analysis revealed that the inserted fragments consisted of the BamHI-W fragment at one end and clone RP11-665A22 on chromosome 15 at the other end. CONCLUSION The successfully established genomic library of Raji cells will provide a basis for cloning the sequences of the EBV junction sites and interpreting the mechanism of oncogenesis of EBV integration.
Base Sequence ; Burkitt Lymphoma ; genetics ; virology ; Chromosomes, Human, Pair 15 ; genetics ; Cloning, Molecular ; DNA Probes ; genetics ; DNA, Viral ; genetics ; Gene Expression Profiling ; Genes, Neoplasm ; genetics ; Genomic Library ; Herpesvirus 4, Human ; genetics ; Humans ; Molecular Sequence Data ; Tumor Cells, Cultured

L-sorbose/L-sorbosone dehydrogenase from Ketogulonigenium vulgare S2 can transform L-sorbose to 2-KLG, which is widely used in production of Vitamin C. In order to obtain the engineering strain producing L-sorbose/L-sorbosone dehydrogenase and simplify the fermentation technology, firstly, this enzyme was purified by the methods of ammonium sulfate precipitation, DEAE Sepharose Fast Flow and Q Sepharose High Performance. Then, the purified L-sorbose/L-sorbosone dehydrogenase was injected to rabbit to obtain antibody. Next, the genomic library of Ketogulonigenium vulgare S2 was constructed by inserting the restriction fragments of chromatosomal DNA digested with Sau3A I into cosmid pKC505 vector digested by Hpa I and Pst I, which were packed with lamda phage package protein and transferred into E. coli DH5alpha in vitro. Finally, the positive strain K719# was selected from more than 12,000 clones via Dot-ELISA. Through the test of SDS-PAGE and thin layer chromatography, the results showed that the engineering strain K719# had the same biological activity as Ketogulonigenium vulgare S2 after adding coenzyme PQQ.
Carbohydrate Dehydrogenases ; genetics ; isolation & purification ; metabolism ; Cloning, Molecular ; Escherichia coli ; genetics ; metabolism ; Genomic Library ; Gluconobacter oxydans ; enzymology ; genetics ; growth & development ; Sorbose ; metabolism ; Sugar Acids ; metabolism ; Transformation, Bacterial

To identify in vivo-induced gene in Streptococcus pneumoniae (S. pn) through a novel in vivo expression technology (IVET), a large promoter-trap library using galU and lacZ as the reporters was constructed. Based on the suicide vector pEVP3, a new vector pEVP3-galU was constructed with promoterless galU gene as an in vivo reporter. Firstly, promoterless galU gene was directly cloned into pEVP3 fusing with promoterless lacZ gene (an in vitro reporter). Then the random pieces of S. pn chromosomal DNA (200-500 bp), obtained by partial Sau3AI restriction digestion, were subcloned into the Bgl II site of pEVP3-galU. Upon introduction of the ligated plasmid library into E. coli DH5alpha by transformation, about 70,000 recombinants were recovered. Considering insert DNA orientation and insert size, this represents 5 coverage of the 2.2 Mb S. pn genome; 90% of these clones had 250- to 500-bp inserts. Thus, the library retained maximal complexity. Transformation by this plasmid library yield 450,000 S. pn transformants. The library was used to infect animals in intraperitoneal model. Those strains survived in vivo while exhibiting a white colony phenotype on TSA agar containing X-gal would indicate that the DNA fragment upstream of the galU reporter contained an in vivo-induced promoter. The promoter-trap library is suitable for screening in vivo-induced gene of S. pn.
Animals ; Cloning, Molecular ; Female ; Genes, Bacterial ; genetics ; Genes, Reporter ; genetics ; Genomic Library ; Mice ; Mice, Inbred BALB C ; Promoter Regions, Genetic ; genetics ; Streptococcus pneumoniae ; genetics

We have constructed a molecular linkage map of pepper (Capsicum spp.) in an interspecific F2 population of 107 plants with 320 RFLP, 136 AFLP, and 46 SSR markers. The resulting linkage map consists of 15 linkage groups covering 1,720 cM with an average map distance of 3.7 cM between framework markers. Most RFLP markers (80%) were pepper-derived clones and these markers were evenly distributed all over the genome. Genes for defense and biosynthesis of carotenoids and capsaicinoids were mapped on this linkage map. By using 30 primer combinations, AFLP markers were generated in the F2 population. For development of SSR markers in Capsicum, microsatellites were isolated from two small-insert genomic libraries and the GenBank database. This combined map provides a starting point for high-resolution QTL analysis, gene isolation, and molecular breeding.
Capsicum ; Carotenoids ; Chromosome Mapping* ; Clone Cells ; Databases, Nucleic Acid ; DNA Shuffling ; Genome* ; Genomic Library ; Microsatellite Repeats ; Polymorphism, Restriction Fragment Length

BACKGROUND: Monoclonal antibodies (mAb) of rodent origin are produced with ease by hybridoma fusion technique, and have been successfully used as therapeutic reagents for humans after humanization by genetic engineering. However, utilization of these antibodies for therapeutic purpose has been limited by the fact that they act as immunogens in human body causing undesired side effects. So far, there have been several attempts to produce human mAbs for effective in vivo diagnostic or therapeutic reagents including the use of humanized xenomouse that is generated by mating knockout mice which lost Ig heavy and light chain genes by homologous recombination and transgenic mice having both human Ig heavy and light gene loci in their genome. METHODS: Genomic DNA fragments of mouse Ig heavy and light chain were obtained from a mouse brain lamda genomic library by PCR screening and cloned into a targeting vector with ultimate goal of generating Ig knockout mouse. RESULTS: Through PCR screening of the genomic library, three heavy chain and three light chain Ig gene fragments were identified, and restriction map of one of the heavy chain gene fragments was determined. Then heavy chain Ig gene fragments were subcloned into a targeting vector. The resulting construct was introduced into embryonic stem cells. Antibiotic selection of transfected cells is under the progress. CONCLUSION: Generation of xenomouse is particularly important in medical biotechnology. However, this goal is not easily achieved due to the technical difficulties as well as huge financial expenses. Although we are in the early stage of a long-term project, our results, at least, partially contribute the successful generation of humanized xenomouse in Korea.
Animals ; Antibodies ; Antibodies, Monoclonal ; Biotechnology ; Brain ; Clone Cells* ; DNA* ; Embryonic Stem Cells ; Gene Knockout Techniques* ; Gene Targeting ; Gene Transfer Techniques ; Genes, Immunoglobulin ; Genetic Engineering ; Genome ; Genomic Library ; Homologous Recombination ; Human Body ; Humans* ; Hybridomas ; Indicators and Reagents ; Korea ; Mass Screening ; Mice* ; Mice, Knockout ; Mice, Transgenic ; Polymerase Chain Reaction ; Rodentia

A pair of degenerate primers were designed based on NBS (nucleotide binding site, NBS) domain of resistance(R) gene and used to perform PCR with cDNA from the translocation line 6VS/6AL of Triticum aestivum-Haynaldia villosa. A clone (N7) characterized with NBS was obtained by sequencing analysis. Two specific primers were designed from the N7 sequence and used to screen a genomic TAC (transformation-competent artificial chromosome, TAC) library of 6VS/6AL consisting of ca. 2 x 10(6) clones. The library was stored as clone pools in twenty-two 96-well plates, each well containing approximately 1000 TAC clones. TAC plasmids were prepared from all the 2112 pools. Using a pooled PCR screening procedure, a positive TAC clone having a 40 kb insert was obtained. The positive clone was confirmed by Southern hybridization with the NBS fragment as a probe. The results indicate that the pooled PCR method is effective for screening of genomic libraries having large number of clones.
Amino Acid Sequence ; Base Sequence ; Binding Sites ; Blotting, Southern ; Chromosomes, Artificial ; Genomic Library ; Molecular Sequence Data ; Polymerase Chain Reaction ; methods ; Translocation, Genetic ; Triticum ; genetics

Porphyromonas gingivalis, a Gram negative, anaerobic, asaccharolytic rod, is one of the most frequently implicated pathogens in human periodontal disease and has a requirement for hemin for growth. A 30 kDa (heated 24 kDa) hemin-binding protein whose expression is both hemin and iron regulated has recently been purified and characterized in this oral pathogen. This study has identified a hemin-binding P. gingivalis protein by expression of a P. gingivalis genomic library in Escherichia coli, a bacterium which does not require or transport exogenous hemin. A library of genomic DNA fragments from P. gingivalis was constructed in plasmid pUC18, transformed into Escherichia coli strain DH5alpha, and screened for recombinant clones with heminbinding activity by plating onto hemin-containing agar. Of approximately 10,000 recombinant E. coli colonies screened on LB-amp-hemin agar, 10 exhibited a clearly pigmented phenotype. Each clone contained various insert DNA. The Hind III fragment transferred to the T7 RNA polymerase/promoter expression vector system produced a sligltly smaller (21 kDa) protein, a precursor form, immunoreactive to the antibody against the 24 kDa protein, suggesting that the cloned DNA fragment probably carried an entire gene for the 24 kDa heminbinding protein.
Agar ; Clone Cells ; DNA ; Escherichia coli ; Genomic Library ; Hemin ; Humans ; Iron ; Periodontal Diseases ; Phenotype ; Plasmids ; Porphyromonas gingivalis* ; Porphyromonas* ; RNA